The custom ones of FF3/5/T were my favourite, but it really depends how they do the customisation - I thought FF7's was rather boring especially since dunking the materia on randomly was still good enough if you don't bother go do side quests such as the weapons. FF8s wasn't bad, although could take quite a while playing around with what each character had to try and optimise everything, I found.

As for the fixed ones, I'd say FF1/9 were the best, since they were more fixed as it were and forced you to use those skills more than say in FF6, where you could end up with everyone learning the same thing.